Comparative proteome profiling of bleomycin‐induced lung toxicity in rats by 2D–nano‐LC–MS/MS and spectral counting

The mechanisms involved in bleomycin‐induced lung toxicity have not been fully understood to date. This work aimed to compare the proteome profiling of bleomycin‐induced lung toxicity by using 2D–nano‐LC–MS/MS and spectral counting. By comparing the spectral counts of identified proteins between control and bleomycin‐treated groups, we noted that 102 proteins were upregulated and 28 proteins were downregulated in the bleomycin‐treated group. Among these differently expressed proteins, five proteins were chosen for validation by Western blot analysis. The levels of these five proteins were consistent with proteomic results. These potential mediators can facilitate the translation of the underlying mechanisms of bleomycin‐induced lung toxicity to molecular targets in the clinical arena.     

Differential expression of proteins in fetal brains of alcohol‐treated prenatally C57BL/6 mice: A proteomic investigation

Alcohol is known to impede the growth of the central nervous system and to induce neurodegeneration through cellular apoptosis. We have previously shown that moderate prenatal alcohol exposure results in brain defects at different stages of development. In this study, we further characterize the proteomic architecture underlying ethanol teratogenesis during early fetal brain development using chromatography in conjunction with a LC‐MS/MS system. Pregnant C57BL/6 mice were exposed from embryonic day 7 (E7) to E13 with either a 25% ethanol derived calorie or pair‐fed liquid diets. At E13, fetal brains were collected from five dams for each group. Individual brains were homogenized and the extracted proteins were then tryptically digested and analyzed by LC‐MS/MS. Label‐free quantitative proteomic analyses were performed on proteomes extracted from fetal brains of both alcohol‐treated (ALC) and pair‐fed groups. These analyses demonstrated that prenatal alcohol exposure induced significant downregulation (p<0.001) of the expression of mitochondrial enzymes including ADP/ATP translocase 1, ATP synthase subunit α and ubiquinol‐cytochrome‐c reductases. In addition, mitochondrial carrier homolog 1, which plays a role in apoptosis, was significantly downregulated (p<0.001) in the ALC group. Moreover, among the cytosolic proteins that were significantly downregulated (p<0.001) are Bcl‐2, 14‐3‐3 protein and calmodulin. Significant downregulation (p<0.001) of proteins that are critical for fetal brain development was observed such as prohibitin and neuronal migration protein doublecortin. These findings provide information about possible mechanisms underlying the effects of prenatal alcohol exposure during early embryonic stage.     

Urinary metabolomics analysis reveals the effect of volatile oil from Angelica sinensis on LPS‐induced inflammation rats

Lipopolysaccharide (LPS)‐induced inflammation occurs commonly and volatile oil from Angelica sinensis (VOAS) can be used as an anti‐inflammatory agent. The molecular mechanisms that allow the anti‐inflammatory factors to be expressed are still unknown. In this paper, we applied gas chromatography–mass spectrometry (GC–MS) and high‐performance liquid chromatography–time‐of‐flight mass spectrometry (LC‐Q/TOF–MS) based on a metabolomics platform coupled with a network approach to analyze urine samples in three groups of rats: one with LPS‐induced inflammation (MI); one with intervention with VOAS; and normal controls (NC). Our study found definite metabolic footprints of inflammation and showed that all three groups of rats, MI, intervention with VOAS and NC have distinct metabolic profiles in urine. The concentrations of 48 metabolites differed significantly among the three groups. The metabolites in urine were screened by the GC–MS and LC‐Q/TOF–MS methods. The significantly changed metabolites (p < 0.05, variable importance in projection > 1.5) between MI, NC and VOAS were included in the metabolic networks. Finally, hub metabolites were screened, including glycine, arachidonic acid, l ‐glutamate, pyruvate and succinate, which have high values of degree (k). the Results suggest that disorders of glycine, arachidonic acid, l ‐glutamate, pyruvate and succinate metabolism might play an important part in the predisposition and development of LPS‐induced inflammation. By applying metabolomics with network methods, the mechanisms of diseases are clearly elucidated.     

Proteomic profiling of mature leaves from oil palm (Elaeis guineensis Jacq.)

Oil palm is one of the most productive oil bearing crops grown in Southeast Asia. Due to the dwindling availability of agricultural land and increasing demand for high yielding oil palm seedlings, clonal propagation is vital to the oil palm industry. Most commonly, leaf explants are used for in vitro micropropagation of oil palm and to optimize this process it is important to unravel the physiological and molecular mechanisms underlying somatic embryo production from leaves. In this study, a proteomic approach was used to determine protein abundance of mature oil palm leaves. To do this, leaf proteins were extracted using TCA/acetone precipitation protocol and separated by 2DE. A total of 191 protein spots were observed on the 2D gels and 67 of the most abundant protein spots that were consistently observed were selected for further analysis with 35 successfully identified using MALDI TOF/TOF MS. The majority of proteins were classified as being involved in photosynthesis, metabolism, cellular biogenesis, stress response, and transport. This study provides the first proteomic assessment of oil palm leaves in this important oil crop and demonstrates the successful identification of selected proteins spots using the Malaysian Palm Oil Board (MPOB) Elaeis guineensis EST and NCBI‐protein databases. The MS data have been deposited in the ProteomeXchange Consortium database with the data set identifier PXD001307.     

Simultaneous determination of atorvastatin,amlodipine, ramipril and benazepril in human plasma by LC‐MS/MS and its application to a human pharmacokinetic study

A rapid, simple, sensitive and specific LC‐MS/MS method has been developed and validated for the simultaneous estimation of atorvastatin (ATO), amlodipine (AML), ramipril (RAM) and benazepril (BEN) using nevirapine as an internal standard (IS). The API‐4000 LC‐MS/MS was operated under the multiple‐reaction monitoring mode using electrospray ionization. Analytes and IS were extracted from plasma by simple liquid–liquid extraction technique using ethyl acetate. The reconstituted samples were chromatographed on C₁₈ column by pumping 0.1% formic acid–acetonitrile (15:85, v/v) at a flow rate of 1 mL/min. A detailed validation of the method was performed as per the FDA guidelines and the standard curves were found to be linear in the range of 0.26–210 ng/mL for ATO; 0.05–20.5 ng/mL for AML; 0.25–208 ng/mL for RAM and 0.74–607 ng/mL for BEN with mean correlation coefficient of ≥0.99 for each analyte. The intra‐day and inter‐day precision and accuracy results were well with in the acceptable limits. A run time of 2.5 min for each sample made it possible to analyze more than 400 human plasma samples per day. The developed assay method was successfully applied to a pharmacokinetic study in human male volunteers. Copyright © 2010 John Wiley & Sons, Ltd.     

Neurotransmitter Transporter Family Including SLC6A6 and SLC6A13 Contributes to the 5‐Aminolevulinic Acid (ALA)‐Induced Accumulation of Protoporphyrin IX and Photodamage,through Uptake of ALA by Cancerous Cells

δ‐Aminolevulinic acid (ALA)‐induced protoporphyrin accumulation is widely used in the treatment of cancer, as photodynamic therapy (PDT). To clarify the mechanisms of ALA uptake by tumor cells, we have examined the ALA‐induced accumulation of protoporphyrin by the treatment of colon cancer DLD‐1 and epithelial cancer HeLa cells with γ‐aminobutyric acid (GABA)‐related compounds. When the cells were treated with GABA, taurine and β‐alanine, the level of protoporphyrin was decreased, suggesting that plasma membrane transporters involved in the transport of neurotransmitters contribute to the uptake of ALA. By transfection with neurotransmitter transporters SLC6A6, SLC6A8 and SLC6A13 cDNA, the ALA‐ and ALA methylester‐dependent accumulation of protoporphyrin markedly increased in HEK293T cells, dependent on an increase in the uptake of ALA. When ALA‐treated cells were exposed to white light, the extent of photodamage increased in SLC6A6‐ and SLC6A13‐expressing cells. Conversely, knockdown of SLC6A6 or SLC6A13 with siRNAs in DLD‐1 and HeLa cells decreased the ALA‐induced accumulation. The expression of SLC6A6 and SLC6A13 was found in some cancer cell lines. Immunohistochemical studies revealed that the presence of these transporters was elevated in colon cancerous cells. These results indicated that neurotransmitter transporters including SLC6A6 and SLC6A13 mediate the uptake of ALA and can play roles in the enhancement of ALA‐induced accumulation of protoporphyrin in cancerous cells.     

Profiling of hydroxyurea-treated β-thalassemia/ serum proteome through nano-LC–ESI–MS/ MS in combination with microsol-isoelectric focusing

Advancements in proteomic tools offer a comprehensive solution to studying the complexity of diseases at molecular level. This study focusses on the clinical proteomic profiling of pre- and post-hydroxyurea (HU)-treated β-thalassemia patients in parallel with healthy individuals to better understand the role of HU in the treatment of β-thalassemia. The strategy encompasses sequential high-resolution protein fractionation using MicroSol-isoelectric focusing (ZOOM- IEF) followed by one-dimensional SDS-PAGE before nano-RP-LC–MS/ MS analysis of tryptic peptides. Protein identification was performed through Mascot search using NCBInr and SwissProt databases. Several different proteins were observed in pool serum samples of each of the three study groups. Approximately, 1250 proteins exclusive to each group were identified, and after removing the redundant and low sequence coverage proteins, the number was reduced to 576 (201 in healthy, 187 in HU-untreated and 188 in HU-treated group). Uniquely identified proteins in the HU-treated group regulate the focal adhesion, ECM-receptor interaction, PI3K-Akt signaling, Rap1 signaling, cAMP signaling, platelet activation, and Ca²⁺ signaling pathways in the HU-treated group. The proteomic profile presented here will add to the current state of understanding of molecular mechanisms involved in hydroxyurea treatment of β-thalassemia.     

Quantification of homocysteine‐related metabolites and the role of betaine–homocysteine S‐methyltransferase in HepG2 cells

We optimized and validated a rapid and sensitive liquid chromatography–tandem mass spectrometry (LC‐MS/MS) method for the quantification of six metabolites of homocysteine metabolism: homocysteine, methionine, cysteine, S‐adenosylmethionine, S‐adenosylhomocysteine and betaine. The detection limits for these metabolites were in the nanomolar range, and the intra‐ and inter‐day precisions were lower than 20% of the relative standard deviations. The method was specifically designed for the determination of the intracellular concentrations of the metabolites in cultured cells. To study the role of betaine–homocysteine S‐methyltransferase (BHMT), HepG2 cells and HepG2 cells that were stably transfected with BHMT (^BHMTHepG2) were treated with homocysteine or with a specific inhibitor of BHMT, and metabolite levels were subsequently measured. Severely compromised methyl group metabolism in the HepG2 cells, which is typical of cancer‐derived cells, prevented clear evaluation of the changes caused by the external manipulations of homocysteine metabolism. However, the ease of handling these cells and the almost unlimited source of experimental material supplied by cells in permanent culture allowed us to develop a reliable methodology. The precautions concerning intracellular metabolite determinations using LC‐MS/MS in cultured cells that are expressed in this work will have global validity for future metabolomics studies. Copyright © 2012 John Wiley & Sons, Ltd.     

Quantification of amlodipine and atorvastatin in human plasma by UPLC–MS/MS method and its application to a bioequivalence study

A robust, rapid and sensitive UPLC–MS/MS method has been developed, optimized and validated for the determination of amlodipine (AML) and atorvastatin (ATO) in human plasma using eplerenone as an internal standard (IS). Multiple‐reaction monitoring in positive electrospray ionization mode was utilized in Xevo TQD LC–MS/MS. Double extraction was used in sample preparation using diethyl ether and ethyl acetate. The prepared samples were analyzed using an Acquity UPLC BEH C₁₈ (50 × 2.1 mm, 1.7 μm) column. Ammonium formate and acetonitrile, pumped isocraticaly at a flow rate of 0.25 mL/min, were used as a mobile phase. Method validation was done as per the US Food and Drug Administration guidelines. Linearity was achieved in the range of 0.1–10 ng/mL for AML and 0.05–50 ng/mL for ATO. Intra‐day and inter‐day accuracy and precision were calculated and found to be within the acceptable range. A short run time, of <1.5 min, permits analysis of a large number of plasma samples per batch. The developed and validated method was applied to estimate AML and ATO in a bioequivalence study in healthy human volunteers.     

Nuclear proteome analysis of undifferentiated mouse embryonic stem and germ cells

Embryonic stem cells (ESCs) and embryonic germ cells (EGCs) provide exciting models for understanding the underlying mechanisms that make a cell pluripotent. Indeed, such understanding would enable dedifferentiation and reprogrammation of any cell type from a patient needing a cell therapy treatment. Proteome analysis has emerged as an important technology for deciphering these biological processes and thereby ESC and EGC proteomes are increasingly studied. Nevertheless, their nuclear proteomes have only been poorly investigated up to now. In order to investigate signaling pathways potentially involved in pluripotency, proteomic analyses have been performed on mouse ESC and EGC nuclear proteins. Nuclei from ESCs and EGCs at undifferentiated stage were purified by subcellular fractionation. After 2‐D separation, a subtractive strategy (subtracting culture environment contaminating spots) was applied and a comparison of ESC, (8.5 day post coïtum (dpc))‐EGC and (11.5 dpc)‐EGC specific nuclear proteomes was performed. A total of 33 ESC, 53 (8.5 dpc)‐EGC, and 36 (11.5 dpc)‐EGC spots were identified by MALDI‐TOF‐MS and/or nano‐LC‐MS/MS. This approach led to the identification of two isoforms (with and without N‐terminal acetylation) of a known pluripotency marker, namely developmental pluripotency associated 5 (DPPA5), which has never been identified before in 2‐D gel‐MS studies of ESCs and EGCs. Furthermore, we demonstrated the efficiency of our subtracting strategy, in association with a nuclear subfractionation by the identification of a new protein (protein arginine N‐methyltransferase 7; PRMT7) behaving as proteins involved in pluripotency.     

Combined usage of cascade affinity fractionation and LC‐MS/MS for the proteomics of adult mouse testis

In this report, the proteomics of adult mouse testis were analyzed by the combined usage of cascade affinity fractionation and LC‐MS/MS. The differences between the selected affinity ligands in size, shape, structure, and biochemical characteristics, result in each ligand exhibiting a specific affinity to some protein groups. Therefore, a cascade composition of different ligands can be applied to the fractionation of complex tissue proteins. Ultimately, the fractions collected from cascade affinity fractionation were analyzed by LC‐MS/MS, which resulted in high confidence identification of a total of 1378 non‐redundant mouse testis protein groups, over 2.6 times as many proteins as were detected in the un‐fractionated sample (526). All detected proteins were bioinformatically categorized according to their physicochemical characteristics (such as relative molecular mass, pI, grand average hydrophobicity value, and transmembrane helices), subcellular location, and function annotation. This approach highlighted the sensitivity of this method to a wide variety of protein classes. Utilizing a combination of cascade affinity fractionation and LC‐MS/MS, we have established the largest proteomic database for adult mouse testis at the present time.     

Cellular proteomic analysis of porcine circovirus type 2 and classical swine fever virus coinfection in porcine kidney‐15 cells using isobaric tags for relative and absolute quantitation‐coupled LC‐MS/MS

Viral coinfection or superinfection in host has caused public health concern and huge economic losses of farming industry. The influence of viral coinfection on cellular protein abundance is essential for viral pathogenesis. Based on a coinfection model for porcine circovirus type 2 (PCV2) and classical swine fever virus (CSFV) developed previously by our laboratory, isobaric tags for relative and absolute quantitation (iTRAQ)‐coupled LC‐MS/MS proteomic profiling was performed to explore the host cell responses to PCV2‐CSFV coinfection. Totally, 3932 proteins were identified in three independent mass spectrometry analyses. Compared with uninfected cells, 304 proteins increased (fold change >1.2) and 198 decreased (fold change <0.833) their abundance in PCV2‐infected cells (p < 0.05), 60 and 61 were more and less abundant in CSFV‐infected cells, and 196 and 158 were more and less abundant, respectively in cells coinfected with PCV2 and CSFV. Representative differentially abundant proteins were validated by quantitative real‐time PCR, Western blotting and confocal laser scanning microscopy. Bioinformatic analyses confirmed the dominant role of PCV2, and indicated that mitochondrial dysfunction, nuclear factor erythroid 2‐related factor 2 (Nrf2)‐mediated oxidative stress response and apoptosis signaling pathways might be the specifical targets during PCV2‐CSFV coinfection.     

A UPLC‐TOF/MS‐based metabolomics study of rattan stems of Schisandra chinensis effects on Alzheimer's disease rats model

A UPLC‐TOF/MS‐based metabolomics method was established to explore the therapeutic mechanisms of rattan stems of S. chinensis (SCS) in Alzheimer's disease (AD). Experimental AD model was induced by intra‐hippocampal Aβ_1–42 injection in rats. Cognitive function and oxidative stress condition in brain of AD rats were assessed using Morris water maze tests and antioxidant assays [malondialdehyde (MDA), superoxide dismutase (SOD) and glutathione peroxidase (GSH‐Px)], respectively. UPLC‐TOF/MS combined with multivariate statistical analysis were conducted to study the changes in metabolic networks in serum of rats. The results indicated that the AD model was established successfully and the inducement of Aβ_1–42 caused a decline in spatial learning and memory of rats. The injection of Aβ_1–42 in rat brains significantly elevated the level of MDA, and reduced SOD and GSH‐Px activities. In addition, SCS showed significant anti‐AD effects on model rats. A total of 30 metabolites were finally identified as potential biomarkers of AD and 14 of them had a significant recovery compared with the AD model after SCS administration. Changes in AD metabolite profiling were restored to different levels through the regulation of 13 pathways. This is first report on the use of the UPLC‐TOF/MS‐based serum metabolomics method to investigate therapeutic effects of SCS on AD, and enrich potential biomarkers and metabolic networks of AD.     

Conductive ATO‐acrylate nanocomposite hybrid coatings: Experimental results and modeling

The electrical volume conductivity σ of antimony‐doped tin oxide (ATO)–acrylate nanocomposite hybrid coatings was investigated. The relation between σ and the volume filler fraction p was analyzed for the ATO‐acrylate coatings containing ATO nanoparticles grafted with different amounts of 3‐methacryloxy‐propyl‐trimethoxy‐silane coupling agent. Percolation thresholds were observed at very low filler fractions (1–2 vol %) for the coatings containing ATO nanoparticles with a low amount of surface grafting. A modified effective medium approximation (EMA) model was introduced. This model takes into consideration different distances between adjacent semiconductive particles in the particle network. The model elucidates how self‐arrangement of the particles influences the location of the percolation threshold in the log σ ? p plot. The modified EMA model can successfully explain the multiple transition behavior and the variable percolation thresholds found for the ATO‐acrylate nanocomposite hybrid coatings. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2147–2160, 2007     

Determination of 12 potential nephrotoxicity biomarkers in rat serum and urine by liquid chromatography with mass spectrometry and its application to renal failure induced by Semen Strychni

In previous nephrotoxicity metabonomic studies, several potential biomarkers were found and evaluated. To investigate the relationship between the nephrotoxicity biomarkers and the therapeutic role of Radix Glycyrrhizae extract on Semen Strychni‐induced renal failure, 12 typical biomarkers are selected and a simple LC–MS method has been developed and validated. Citric acid, guanidinosuccinic acid, taurine, guanidinoacetic acid, uric acid, creatinine, hippuric acid, xanthurenic acid, kynurenic acid, 3‐indoxyl sulfate, indole‐3‐acetic acid, and phenaceturic acid were separated by a Phenomenex Luna C₁₈ column and a methanol/water (5 mM ammonium acetate) gradient program with a runtime of 20 min. The prepared calibration curves showed good linearity with regression coefficients all above 0.9913. The absolute recoveries of analytes from serum and urine were all more than 70.4%. With the developed method, analytes were successfully determined in serum and urine samples within 52 days. Results showed that guanidinosuccinic acid, guanidinoacetic acid, 3‐indoxyl sulfate, and indole‐3‐acetic acid (only in urine) were more sensitive than the conventional renal function markers in evaluating the therapeutic role of Radix Glycyrrhizae extract on Semen Strychni‐induced renal failure. The method could be further used in predicting and monitoring renal failure cause by other reasons in the following researches.